X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details Protein (15 mM Bis-Tris, 500 mM NaCl, 10% glycerol, 5 mM DTT, 200 mM 4-OH PROLINE, TEV Treated, Cleavage Unverified); Reservoir (0.1 M NaAcetate, 25% Peg4000, 8% 2-propanol (MCSG4 H2)); Cryoprotection (Reservoir+20% isopropanaol) , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 178.01 α = 90
b = 178.01 β = 90
c = 49.74 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE MIRRORS 2012-06-12
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.7 125.88 99.9 0.078 0.078 -- 10.4 88126 88126 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.79 99.9 0.745 0.745 1.0 7.9 12695

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.7 33.165 0.0 1.34 87548 87548 4395 99.31 -- 0.1594 0.1576 0.1919 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.7193 -- 149 2724 0.2291 0.2729 -- 100.0
X Ray Diffraction 1.7193 1.7395 -- 147 2719 0.2142 0.2861 -- 100.0
X Ray Diffraction 1.7395 1.7608 -- 126 2802 0.2051 0.2319 -- 100.0
X Ray Diffraction 1.7608 1.783 -- 143 2768 0.1953 0.2282 -- 100.0
X Ray Diffraction 1.783 1.8065 -- 129 2718 0.1903 0.2209 -- 100.0
X Ray Diffraction 1.8065 1.8313 -- 161 2778 0.1841 0.2526 -- 100.0
X Ray Diffraction 1.8313 1.8574 -- 158 2723 0.1821 0.246 -- 100.0
X Ray Diffraction 1.8574 1.8851 -- 133 2754 0.2122 0.2508 -- 100.0
X Ray Diffraction 1.8851 1.9146 -- 144 2667 0.3108 0.3745 -- 96.0
X Ray Diffraction 1.9146 1.946 -- 141 2646 0.3178 0.3826 -- 97.0
X Ray Diffraction 1.946 1.9795 -- 135 2775 0.1842 0.2133 -- 100.0
X Ray Diffraction 1.9795 2.0155 -- 137 2758 0.1621 0.1879 -- 100.0
X Ray Diffraction 2.0155 2.0543 -- 137 2784 0.1717 0.2359 -- 100.0
X Ray Diffraction 2.0543 2.0962 -- 150 2705 0.2191 0.2698 -- 99.0
X Ray Diffraction 2.0962 2.1418 -- 148 2751 0.1507 0.1898 -- 100.0
X Ray Diffraction 2.1418 2.1916 -- 135 2811 0.1478 0.2014 -- 100.0
X Ray Diffraction 2.1916 2.2464 -- 154 2662 0.1924 0.2487 -- 97.0
X Ray Diffraction 2.2464 2.3071 -- 142 2657 0.2061 0.2359 -- 96.0
X Ray Diffraction 2.3071 2.375 -- 163 2801 0.1379 0.197 -- 100.0
X Ray Diffraction 2.375 2.4516 -- 141 2746 0.131 0.1564 -- 100.0
X Ray Diffraction 2.4516 2.5392 -- 149 2797 0.1289 0.1762 -- 100.0
X Ray Diffraction 2.5392 2.6408 -- 154 2811 0.1227 0.1636 -- 100.0
X Ray Diffraction 2.6408 2.761 -- 169 2786 0.1348 0.16 -- 100.0
X Ray Diffraction 2.761 2.9064 -- 120 2810 0.1316 0.1734 -- 100.0
X Ray Diffraction 2.9064 3.0884 -- 146 2824 0.1389 0.1565 -- 100.0
X Ray Diffraction 3.0884 3.3267 -- 169 2808 0.1368 0.1472 -- 100.0
X Ray Diffraction 3.3267 3.6611 -- 166 2800 0.1372 0.1874 -- 100.0
X Ray Diffraction 3.6611 4.1899 -- 151 2849 0.1373 0.1496 -- 99.0
X Ray Diffraction 4.1899 5.2755 -- 154 2892 0.117 0.1357 -- 100.0
X Ray Diffraction 5.2755 33.1709 -- 144 3027 0.1636 0.1918 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.1106
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.081
f_dihedral_angle_d 13.522
f_bond_d 0.01
f_angle_d 1.32
f_plane_restr 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5173
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 699

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
MOSFLM data reduction
AMoRE phasing